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@g2nb Genomics to Notebook

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    42 repositories

    • notebook-projects

      Public
      Code for notebook project publishing and sharing
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • nbtools

      Public
      A framework for creating user-friendly widgets and tools in Jupyter
      pythonjupyternbextension
      pythonjupyternbextensionlabextension
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•18•1•0•Updated Oct 10, 2024Oct 10, 2024

    • galahad

      Public
      Connect to the Galaxy platform within Jupyter notebooks.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • ipyuploads

      Public
      A Jupyter file widget with improved upload capabilities
      pythonjupyterupload
      pythonjupyteruploadipywidgets
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•2•0•Updated Oct 10, 2024Oct 10, 2024

    • docs

      Public
      Documentation website for genomics 2 notebook (g2nb)
      1•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • jupyter-wysiwyg

      Public
      A rich text editor for markdown cells in Jupyter
      jupyterwysiwyg-editornbextension
      jupyterwysiwyg-editornbextensionlabextension
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •11•55•4•0•Updated Dec 11, 2023Dec 11, 2023

    • website

      Public
      Temporary location of the website for testing
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

    • hub-theme

      Public
      g2nb theme for JupyterHub
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • visualizers

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 27, 2023Oct 27, 2023

    • jupyterlab-theme

      Public
      A theme extension for JupyterLab with the g2nb logo and colors
      CSS
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • multiauthenticator

      Public
      Authenticate JupyterHub with multiple services
      jupyterhubauthenticator
      jupyterhubauthenticator
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 7, 2023Aug 7, 2023

    • guestauthenticator

      Public
      Sign in to JupyterHub using anonymous guest credentials
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 2, 2023Aug 2, 2023

    • g2nb

      Public
      Meta-package for installing all of the g2nb tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•0•0•Updated Jul 24, 2023Jul 24, 2023

    • cywidget

      Public
      A user-friend widget that accepts a Cytoscape file and visualizes the network
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Apr 18, 2023Apr 18, 2023

    • fastawidget

      Public
      Widget that displays a FASTA file
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 22, 2023Feb 22, 2023

    • igv-jupyter

      Public
      Extension for Jupyter which integrates igv.js
      visualizationjupyterlabextension
      visualizationjupyterlabextension
      JavaScript
      •
      MIT License
      •12•154•2•0•Updated Jan 3, 2023Jan 3, 2023

    • tutorial-notebooks

      Public
      Jupyter notebooks for the g2nb project
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Census-of-Immune-Cells-Single-Cell-Workflow-with-CoGAPS

      Public
      Demonstrates how to preprocess and analyze a large single-cell dataset, This version of the notebook includes all the Python and R code used for the analysis
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Genomic-Discovery-to-Translation

      Public
      Identify cancer subtype specific compounds using DiSCoVER (Hanaford et al, Clinical Cancer Research, 2016)
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • ITCR2019-Drug-Recommendations-Using-DiSCoVER

      Public
      Notebook used for ITCR2019 by EFJ
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • The-AMARETTO-framework-in-GenePattern-Notebook

      Public
      Multiscale and multimodal inference of regulatory networks to identify cell circuits and their drivers shared/distinct within/across biological systems of human…
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Single-Cell-RNA-seq-Clustering-Analysis-Notebook

      Public
      Preprocessing and clustering for single cell RNA-seq data
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Cell-Migration-Quantification

      Public
      Quantify cell migration for circular migration regions
      Jupyter Notebook
      •0•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • Methylation-Array-CNV-Analysis

      Public
      Perform Copy Number Variation Analysis on Illumina 450k/EPIC methylation array data.
      Jupyter Notebook
      •0•1•0•0•Updated Jan 21, 2022Jan 21, 2022

    • Differential-expression

      Public
      Perform differential expression.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • GenePattern-Notebook-Analysis-Template

      Public
      A best-practices template notebook for authoring GenePattern Notebook analyses.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • volcano-plot

      Public
      Make a simple volcano plot
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

    • seurat-suite

      Public
      QC, preprocessing, clustering, and visualization of scRNA-seq data using Seurat.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 14, 2022Jan 14, 2022

    • do-et-alli-20201

      Public
      Companion project to the publication A FZD7-specific antibody-drug conjugate induces solid tumor regression in preclinical models by Myan Do et al.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Jan 14, 2022Jan 14, 2022

    • workshop-notebooks

      Public
      Jupyter notebooks intended for g2nb workshops
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 14, 2022Jan 14, 2022
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